Process fish surveys

Author

Juan Mayorga

Published

March 26, 2024

Code
library(ggtext)
library(paletteer)
library(sf)
library(terra)
library(tidyverse)
library(gt)
library(DBI)
library(bigrquery)

knitr::opts_chunk$set(eval = T, warning = F, message = F, include = T, echo = F)

PristineSeasR::set_ps_paths(email = "marine.data.science@ngs.org")

exp_path <- file.path(ps_science_path, "expeditions", "Niue-2023")

ps_data_path <- file.path(ps_science_path, "datasets/")

bq_auth(email = "marine.data.science@ngs.org")

bq_connection <- dbConnect(bigquery(), 
                           project = "pristine-seas")

1 Metadata

Number of stations per region, habitat, and exposure
habitat exposure n_stations n_strata n_transects
Antiope
Forereef Windward 2 1 12
Beveridge
Backreef Lagoon 5 1 20
Forereef Leeward 5 2 30
Forereef Windward 7 2 42
Niue
Forereef Leeward 13 2 64

2 Data processsing

2.1 Observations

2.2 Clean taxa

2.3 Calculate biomass

2.4 DB Upload

3 Analyses

3.1 By location

Number of workstations and average species richness (# species/station-strata), fish abundance (ind/m2), and biomass (g/m2) for each location
location stations transects n_taxa ind_m2 gr_m2
Antiope 2 12 17.00 0.47 36.97
Beveridge 17 92 37.12 2.16 270.94
Niue 13 64 41.35 2.18 75.56

3.2 By depth strata

Number of workstations and average species richness (# species/station-strata), fish abundance (ind/m2), and biomass (g/m2) for each location and depth strata
Location/Strata stations transects n_taxa ind_m2 gr_m2
Antiope
Shallow 2 12 17.00 0.47 36.97
Beveridge
Deep 12 36 42.67 2.10 256.58
Shallow 12 36 37.33 2.28 183.87
Supershallow 5 20 30.20 2.10 392.66
Niue
Deep 13 32 40.62 2.09 71.97
Shallow 13 32 42.08 2.27 79.16

3.3 By exposure

Number of workstations and average species richness (# species/station-strata), fish abundance (ind/m2), and biomass (g/m2) for each location and exposure
Location/Strata stations transects n_taxa ind_m2 gr_m2
Antiope
Windward 2 12 17.00 0.47 36.97
Beveridge
Lagoon 5 20 30.20 2.10 392.66
Leeward 5 30 39.60 2.33 154.53
Windward 7 42 40.29 2.09 267.15
Niue
Leeward 13 64 41.35 2.18 75.56

3.4 By habitat

Number of workstations and average species richness (# species/station-strata), fish abundance (ind/m2), and biomass (g/m2) for each location and habitat
Location/Strata stations transects n_taxa ind_m2 gr_m2
Antiope
Forereef 2 12 17.00 0.47 36.97
Beveridge
Backreef 5 20 30.20 2.10 392.66
Forereef 12 72 40.00 2.19 220.23
Niue
Forereef 13 64 41.35 2.18 75.56

3.5 Univariate adonis

Results of Adonis model for univariate analysis of fish species richness
df SumOfSqs R2 statistic p.value
depth_strata 1 40.500 0.006 0.636 0.463
location 2 1489.737 0.230 11.688 0.001
exposure 1 2.743 0.000 0.043 0.828
habitat 0 0.000 0.000 Inf NA
Residual 58 3696.242 0.570 NA NA
Total 63 6487.609 1.000 NA NA
Results of Adonis model for univariate analysis of fish abundance
df SumOfSqs R2 statistic p.value
depth_strata 1 0.396 0.007 0.516 0.483
location 2 8.688 0.155 5.657 0.005
exposure 1 0.335 0.006 0.436 0.507
habitat 0 0.000 0.000 Inf NA
Residual 58 44.542 0.793 NA NA
Total 63 56.151 1.000 NA NA
Results of Adonis model for univariate analysis of fish biomass
df SumOfSqs R2 statistic p.value
depth_strata 1 12138.26 0.004 0.392 0.541
location 2 179920.08 0.066 2.909 0.069
exposure 1 73987.53 0.027 2.392 0.126
habitat 0 0.00 0.000 Inf NA
Residual 58 1793727.50 0.656 NA NA
Total 63 2735734.88 1.000 NA NA

3.6 By family

Number of families, species, total abundance (ind/m2) and biomass (g/m2) by taxonmic order
Class/Order family n_genus n_species total_abundance total_biomass
Teleostei
Acanthuriformes Acanthuridae 4 25 0.358 45.617
Eupercaria incertae sedis Scaridae 4 10 0.023 24.665
Centrarchiformes Kyphosidae 1 1 0.022 17.496
Perciformes Serranidae 8 12 0.128 7.412
Eupercaria incertae sedis Lutjanidae 4 5 0.014 7.295
Mulliformes Mullidae 2 6 0.029 6.348
Carangiformes Carangidae 4 6 0.005 5.318
Tetraodontiformes Balistidae 5 8 0.021 4.751
Eupercaria incertae sedis Labridae 18 33 0.208 4.559
Eupercaria incertae sedis Lethrinidae 2 2 0.007 4.213
Ovalentaria incertae sedis Pomacentridae 9 21 0.986 3.505
Holocentriformes Holocentridae 3 4 0.014 3.256
Acanthuriformes Chaetodontidae 3 17 0.058 2.915
Carangaria incertae sedis Sphyraenidae 1 2 0.002 2.306
Acanthuriformes Pomacanthidae 3 6 0.067 1.400
Centrarchiformes Cirrhitidae 4 6 0.078 0.873
Syngnathiformes Fistulariidae 1 1 0.000 0.397
Tetraodontiformes Monacanthidae 1 2 0.000 0.358
Eupercaria incertae sedis Haemulidae 1 1 0.000 0.304
Acanthuriformes Zanclidae 1 1 0.002 0.302
Anguilliformes Muraenidae 1 2 0.000 0.243
Tetraodontiformes Tetraodontidae 2 2 0.001 0.148
Perciformes Pinguipedidae 1 3 0.002 0.104
Perciformes Scorpaenidae 1 2 0.000 0.058
Tetraodontiformes Diodontidae 1 1 0.000 0.034
Gobiiformes Microdesmidae 2 2 0.025 0.030
Blenniiformes Blenniidae 2 3 0.013 0.023
Aulopiformes Synodontidae 1 1 0.000 0.020
Kurtiformes Apogonidae 1 1 0.001 0.008
Elasmobranchii
Carcharhiniformes Carcharhinidae 2 2 0.001 32.987

3.7 By trophic group

3.8 By species

Fish abundance (ind/m2), biomass (g/m2), and frequency of observation (% strata)

3.9 Community composition

Results of community composition adonis model
term df SumOfSqs R2 statistic p.value
location 2 2.327 0.102 4.279 0.001
exposure 1 1.305 0.057 4.800 0.001
habitat 0 0.000 0.000 Inf NA
depth_strata 1 0.563 0.025 2.070 0.012
Residual 58 15.769 0.689 NA NA
Total 63 22.900 1.000 NA NA
Overall fit of the ordination model
term df SumOfSqs statistic p.value
Model 4 6.924 4.735 0.001
Residual 59 21.567 NA NA
Significance of each axis in the ordination model
term df SumOfSqs statistic p.value
dbRDA1 1 3.058 8.365 0.001
dbRDA2 1 1.811 4.954 0.001
dbRDA3 1 1.372 3.753 0.001
dbRDA4 1 0.683 1.870 0.001
Residual 59 21.567 NA NA
Significace of each term in the ordination model
term df SumOfSqs statistic p.value
location 2 3.805 5.205 0.001
exposure 2 3.119 4.266 0.001
Residual 59 21.567 NA NA

3.10 Changes since 2016

Changes in fish biomass by location and depth strata (2016-2023)
Location/Strata 2016 2023
Beveridge
Deep 162.77 256.58
Shallow 95.90 183.87
Supershallow 74.94 392.66
Niue
Deep 46.03 71.97
Shallow 62.89 79.16
Supershallow 78.62 NA

Results of Adonis model for univariate analysis of fish diversity
term df SumOfSqs R2 statistic p.value
depth_strata 2 48508.018 0.014 1.424 0.250
habitat 1 1322.878 0.000 0.078 0.767
location 2 339187.897 0.100 9.960 0.007
year 1 282385.038 0.083 16.585 0.001
Residual 144 2451879.323 0.724 NA NA
Total 150 3387213.191 1.000 NA NA